Ecosyste.ms: Issues

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GitHub / claraqin/neonmicrobe issues and pull requests

#45 - CyVerse test using `analyze-neon-greatplains-16s.R`

Issue - State: open - Opened by KaiZhuPhD over 3 years ago - 3 comments

#44 - Install Rhtslib error

Issue - State: closed - Opened by KaiZhuPhD over 3 years ago - 2 comments

#43 - Batch structure

Pull Request - State: closed - Opened by claraqin over 3 years ago

#42 - created R package structure

Pull Request - State: closed - Opened by claraqin over 3 years ago - 1 comment

#40 - Meta reliant utils

Pull Request - State: closed - Opened by claraqin over 3 years ago

#39 - Ensure that code involving NEON soil data products still works

Issue - State: closed - Opened by claraqin over 3 years ago - 4 comments

#38 - Error in downloadRawSoilData()

Issue - State: closed - Opened by claraqin almost 4 years ago - 5 comments

#37 - Better associations between metadata and sequence data

Issue - State: closed - Opened by claraqin almost 4 years ago - 6 comments

#36 - Replace filename-parsing code with metadata-matching code in all vignettes

Issue - State: closed - Opened by claraqin almost 4 years ago - 1 comment

#35 - Have params printed to screen conspicuously at some point

Issue - State: closed - Opened by claraqin almost 4 years ago - 1 comment

#34 - Change output directory structure

Issue - State: closed - Opened by claraqin almost 4 years ago - 1 comment

#33 - Help Clara test her GitHub notifications!

Issue - State: closed - Opened by claraqin almost 4 years ago - 1 comment

#32 - Add verbose flag to downloadRawSequenceData()

Issue - State: closed - Opened by claraqin almost 4 years ago - 1 comment

#30 - Make pipeline robust to changing file naming conventions

Issue - State: closed - Opened by claraqin almost 4 years ago - 2 comments

#29 - Metadata/downloading QC checklist

Issue - State: open - Opened by claraqin almost 4 years ago - 6 comments

#28 - can't knit vignette download-neon-data

Issue - State: closed - Opened by lstanish about 4 years ago - 4 comments

#27 - Instructions for pipeline testing

Issue - State: open - Opened by claraqin about 4 years ago - 3 comments

#26 - Pipeline testing on Windows

Issue - State: open - Opened by KaiZhuPhD about 4 years ago - 8 comments

#25 - Include variable name descriptions in workflow

Issue - State: closed - Opened by claraqin about 4 years ago

#24 - Follow R package conventions for directory structure

Issue - State: closed - Opened by claraqin about 4 years ago - 2 comments

#23 - Make remove_unmatched_files() robust to differences in file naming convention

Issue - State: closed - Opened by claraqin about 4 years ago - 1 comment

#21 - Fastq files must be in fastq.gz format for sequence processing pipeline

Issue - State: closed - Opened by claraqin about 4 years ago - 2 comments

#20 - Update the vignettes to remove chimeras AFTER merging sequence tables

Issue - State: closed - Opened by claraqin about 4 years ago - 5 comments

#19 - Option to exclude legacy data and other dataQF tags

Issue - State: closed - Opened by claraqin about 4 years ago - 3 comments

#18 - organizeRawSequenceData should sort ITS/16S based on metadata

Issue - State: closed - Opened by claraqin about 4 years ago - 2 comments

#17 - Sequence downloading functions should utilize neonUtilities::zipsByURI

Issue - State: closed - Opened by claraqin about 4 years ago - 2 comments

#15 - Create vignette for sensitivity analysis

Issue - State: closed - Opened by claraqin about 4 years ago

#14 - Simplify directory construction using system commands

Issue - State: closed - Opened by zoey-rw over 4 years ago - 2 comments

#13 - Soil database construction cannot handle missing data

Issue - State: closed - Opened by zoey-rw over 4 years ago - 3 comments

#12 - began workaround

Pull Request - State: closed - Opened by claraqin over 4 years ago

#11 - Separate runs

Pull Request - State: closed - Opened by claraqin over 4 years ago

#10 - Test

Pull Request - State: closed - Opened by claraqin over 4 years ago

#9 - Some fastq file URLs return 404 error

Issue - State: closed - Opened by claraqin over 4 years ago - 1 comment

#8 - Make selective downloading more robust

Issue - State: closed - Opened by claraqin over 4 years ago - 7 comments

#7 - DADA2::filterAndTrim removes majority of ITS reads

Issue - State: closed - Opened by claraqin over 4 years ago - 3 comments

#6 - Error tolerance of cutadapt should also be a parameter

Issue - State: open - Opened by claraqin over 4 years ago - 3 comments

#5 - Mixed orientation of reads in R1 and R2 files

Issue - State: closed - Opened by claraqin over 4 years ago - 2 comments

#4 - Read fastq.gz file

Issue - State: closed - Opened by KaiZhuPhD over 4 years ago - 1 comment

#3 - Project management

Issue - State: closed - Opened by KaiZhuPhD over 4 years ago

#2 - New server setup data download

Issue - State: closed - Opened by yyachung almost 5 years ago - 4 comments

#1 - Data folders

Issue - State: closed - Opened by KaiZhuPhD about 5 years ago - 1 comment